Deacylation Reaction Research Articles

Effect of acyl chain length on selective biocatalytic deacylation on O-aryl glycosides and separation of anomers

It has been demonstrated that Lipozyme® TL IM (Thermomyces lanuginosus lipase immobilised on silica) can selectively deacylate the ester function involving the C-5′ hydroxyl group of α-anomers over the other acyl functions of anomeric mixture of peracylated O-aryl α,β-D-ribofuranoside. The analysis of results of biocatalytic deacylation reaction revealed that the reaction time decreases with the increase in the acyl chain length from C1 to C4. The unique selectivity of Lipozyme® TL IM has been harnessed for the separation of anomeric mixture of peracylated O-aryl α,β-D-ribofuranosides, The lipase mediated selective deacylation methodology has been used for the synthesis of O-aryl α-D-ribofuranosides and O-aryl β-D-ribofuranosides in pure forms, which can be used as chromogenic substrate for the detection of pathogenic microbial parasites containing glycosidases.

Metal-Free Synthesis of 2-Oxindoles via PhI(OAc)2-Mediated Oxidative C–C Bond Formation

The series of 3-monofunctionalized 2-oxindoles 2 were conveniently synthesized from reactions between anilide 1 and phenyliodine(III) diacetate (PIDA) through hypervalent iodine mediated C(sp2)–C(sp2) bond formation followed by a subsequent deacylation reaction. This metal-free method, shown to provide direct access to an important oxindole intermediate, could be applied to the total synthesis of naturally occurring horsfiline.

Polymers containing imidazole groups as nanoreactors for hydrolysis of esters

A polymer (PAIM) containing the functional groups imidazole and carboxylic acid acts as a nanoreactor to accelerate deacylation and dephosphorylation reactions. The synthesis was designed to position the two functional groups next to each other, allowing cooperativity. The catalytic efficiency of the polymer was evaluated for the hydrolytic cleavage of p‐nitrophenyl acetate (PNPA) and diethyl 2,4‐dinitrophenyl phosphate (DEDNPP). PAIM was both efficient and promiscuous, increasing the rates of all reactions up to 107‐fold. Copyright © 2014 John Wiley & Sons, Ltd.

Study on the thermal degradation of 3-MCPD esters in model systems simulating deodorization of vegetable oils

The establishment of effective strategies for the mitigation of 3-MCPD esters in refined vegetable oils is restricted by limited knowledge of their mechanisms of formation and decomposition. In order to gain better understanding on the thermal stability of these compounds, a model system for mimicking oil refining conditions was developed. Pure 3-MCPD esters (3-MCPD dipalmitate and 3-MCPD dilaurate) were subjected to thermal treatment (180–260°C) and the degradation products where monitored over time (0–24h). After 24h of treatment, both 3-MCPD esters showed a significant degradation (ranging from 30% to 70%), correlating with the temperature applied. The degradation pathway, similar for both compounds, was found to involve isomerisation (very rapid, equilibrium was reached within 2h at 260°C), dechlorination and deacylation reactions. The higher relative abundance of non-chlorinated compounds, namely acylglycerols, in the first stages of the treatment suggested that dechlorination is preferred over deacylation with the conditions applied in this study.

Structural basis for the β-lactamase activity of EstU1, a family VIII carboxylesterase

EstU1 is a unique family VIII carboxylesterase that displays hydrolytic activity toward the amide bond of clinically used β-lactam antibiotics as well as the ester bond of p-nitrophenyl esters. EstU1 assumes a β-lactamase-like modular architecture and contains the residues Ser100, Lys103, and Tyr218, which correspond to the three catalytic residues (Ser64, Lys67, and Tyr150, respectively) of class C β-lactamases. The structure of the EstU1/cephalothin complex demonstrates that the active site of EstU1 is not ideally tailored to perform an efficient deacylation reaction during the hydrolysis of β-lactam antibiotics. This result explains the weak β-lactamase activity of EstU1 compared with class C β-lactamases. Finally, structural and sequential comparison of EstU1 with other family VIII carboxylesterases elucidates an operative molecular strategy used by family VIII carboxylesterases to extend their substrate spectrum.

QM/MM and free-energy simulations of deacylation reaction catalysed by sedolisin, a serine-carboxyl peptidase

Quantum mechanical/molecular mechanical free-energy simulations were performed to understand the deacylation reaction catalysed by sedolisin (a serine-carboxyl peptidase) and to elucidate the catalytic mechanism and the role of the active-site residues during the process. The results given here demonstrate that Asp170 may act as a general acid/base catalyst for the deacylation reaction. It is also shown that the electrostatic oxyanion hole interactions involving Asp170 may be less effective in transition state stabilisation for the deacylation step in the sedolisin-catalysed reaction compared to the general acid/base mechanism. The proton transfer processes during the enzyme-catalysed process were examined, and their role in the catalysis was discussed.

Efficient α-chlorination of 2-[(1-oxocyclohex-2-en-2-yl)methyl]-1,3-dicarbonyl Compounds Using Sodium Hypochlorite

A rapid and efficient regioselective α-chlorination of a new series of β-dicarbonyl compounds using a commercial solution of sodium hypochlorite in the presence of K2CO3 in THF at 0 °C, is reported. With prolonged reaction times, α-chloro β-keto esters, bearing an acyl moiety, undergo a tandem chlorination–deacylation reaction, affording the corresponding α-chlorinated esters.

Crystal structure of 6-guanidinohexanoyl trypsin near the optimum pH reveals the acyl-enzyme intermediate to be deacylated

The force driving the conversion from the acyl intermediate to the tetrahedral intermediate in the deacylation reaction of serine proteases remains unclear. The crystal structure of 6-guanidinohexanoyl trypsin was determined at pH 7.0, near the optimum reaction pH, at 1.94 Å resolution. In this structure, three water molecules are observed around the catalytic site. One acts as a nucleophile to attack the acyl carbonyl carbon while the other two waters fix the position of the catalytic water through a hydrogen bond. When the acyl carbonyl oxygen oscillates thermally, the water assumes an appropriate angle to catalyze the deacylation.

The Bicyclic Intermediate Structure Provides Insights into the Desuccinylation Mechanism of Human Sirtuin 5 (SIRT5)

Sirtuins are pivotal regulators in various cellular processes, including transcription, DNA repair, genome stability, and energy metabolism. Their functions have been generally attributed to NAD-dependent deacetylase activity. However, human SIRT5 (sirtuin 5), which has been reported to exhibit little deacetylase activity, was recently identified as an NAD-dependent demalonylase and desuccinylase. Biochemical studies suggested that the mechanism of SIRT5-catalyzed demalonylation and desuccinylation is similar to that of deacetylation catalyzed by other sirtuins. Previously, we solved the crystal structure of a SIRT5-succinyl-lysine peptide-NAD complex. Here, we present two more structures: a binary complex of SIRT5 with an H3K9 succinyl peptide and a binary complex of SIRT5 with a bicyclic intermediate obtained by incubating SIRT5-H3K9 thiosuccinyl peptide co-crystals with NAD. To our knowledge, this represents the first bicyclic intermediate for a sirtuin-catalyzed deacylation reaction that has been captured in a crystal structure, thus providing unique insights into the reaction mechanism. The structural information should benefit the design of specific inhibitors for SIRT5 and help in exploring the therapeutic potential of targeting sirtuins for treating human diseases.

Biocatalytic Deacylation Studies on Tetra-O-acyl-β-d-xylofuranosyl Nucleosides: Synthesis of xylo-LNA Monomers

A Novozyme-435 catalytic methodology has been developed for selective deacylation of one of the acyloxy functions involving a primary -OH group over the other acyloxy functions involving primary and secondary -OH groups in 4'-C-acyloxymethyl-2',3',5'-tri-O-acyl-β-D-xylofuranosyl nucleosides. Optimization of the biocatalytic reaction revealed that tetra-O-butanoyl-β-D-xylofuranosyl nucleosides are the best substrates for the enzyme. The possibility of acyl migration during enzymatic deacylation reactions has been ruled out by carrying out biocatalytic deacylation reactions on mixed esters of 4'-C-hydroxymethyl-2',3',5'-tri-O-acetyl-β-D-xylofuranosyl nucleosides. The developed methodology has been used for the efficient synthesis of xylo-LNA monomers T, U, A, and C in good yields.

An expedient biocatalytic procedure for abasic site precursors useful in oligonucleotide synthesis

Preparation of abasic site precursors through a divergent chemoenzymatic synthesis has been accomplished. Several biocatalysts and acylating agents were studied furnishing a practical and scalable green method useful for industrial applications. Highly regioselective acylation and deacylation reactions with 1,2-dideoxy-D-ribose are described resulting in excellent yield. A fast, atom-efficient and convenient synthesis of 3-, and 5-O-DMTr-1,2-dideoxyribose 17 and 19 has been achieved. These compounds are useful precursors for the preparation of phosphoramidites required for the assembly of oligonucleotides containing the tetrahydrofuran abasic lesions.

Understanding the Mechanism of Deacylation Reaction Catalyzed by the Serine Carboxyl Peptidase Kumamolisin-As: Insights from QM/MM Free Energy Simulations

Quantum mechanical/molecular mechanical (QM/MM) molecular dynamics and free energy simulations are performed to study the process of the deacylation reaction catalyzed by kumamolisin-As, a serine-carboxyl peptidase, and to elucidate the catalytic mechanism. The results given here suggest that Asp-164 acts as a general acid/base catalyst not only for the acylation reaction but also for the deacylation reaction. It is shown that the electrostatic oxyanion hole interactions may be less effective in transition state stabilization for the kumamolisin-As catalyzed reaction compared to the general acid/base mechanism involving the proton transfer from or to Asp-164. The dynamic substrate-assisted catalysis (DSAC) involving His at the P1 site of the substrate is found to be less important for the deacylation reaction than for the acylation reaction in the kumamolisin-As catalyzed reaction. The proton transfer processes during the enzyme-catalyzed process are examined and their role in the catalysis is discussed.

Lipase-Catalyzed Oligomerization and Hydrolysis of Alkyl Lactates: Direct Evidence in the Catalysis Mechanism That Enantioselection Is Governed by a Deacylation Step

Lipase-catalyzed oligomerization of alkyl d- and l-lactate monomers (RDLa and RLLa, respectively) was studied for the first time. It has been found that the oligomerization occurs enantioselectively only for d-lactates to give oligomers up to heptamers of lactic acid (LA) in good to high yields by using primary C1 to C8 alkyl groups and sec-butyl group for d-lactate monomers. No reaction happened for all l-lactates in similar conditions. Lipase-catalyzed hydrolysis of alkyl d- and l-lactates was also examined, revealing that the hydrolysis took place for both d- and l-lactates, although l-lactates proceeded a couple of times slower. The hydrolysis results clearly demonstrate that the lipase catalysis mechanism involves an acyl-enzyme intermediate (EM) formation via the acylation step from both d- and l-lactates as a rate-determining step, and the subsequent deacylation step, a nucleophilic attack of water to the EM, takes place to produce free LA. On the other hand, in the oligomerization of d-lactates, the deacylation step, in which a sec-alcohol group of the monomer or of the propagating chain-end attacks to the EM, is only allowed for the sec-d-alcohol group to give a one-LA-unit-elongated oligomer. l-Lactates form the EM; however, the subsequent deacylation reaction with both the sec-l- and sec-d-alcohol groups does not take place, failing in the oligomerization to occur. These results provide with the first direct evidence in the lipase catalysis that the enantioselection is governed by the deacylation step. In the co-oligomerization between l- and d-lactates, the l-isomer retarded the reaction rate of the d-isomer, which was found due to the function of the former as a competitive inhibitor in the acylation step toward the latter.

Catalytic Reaction Mechanism of Acetylcholinesterase Determined by Born−Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations

Acetylcholinesterase (AChE) is a remarkably efficient serine hydrolase responsible for the termination of impulse signaling at cholinergic synapses. By employing Born-Oppenheimer molecular dynamics simulations with a B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized its complete catalytic reaction mechanism for hydrolyzing neurotransmitter acetylcholine (ACh) and determined its multistep free-energy reaction profiles for the first time. In both acylation and deacylation reaction stages, the first step involves the nucleophilic attack on the carbonyl carbon, with the triad His447 serving as the general base, and leads to a tetrahedral covalent intermediate stabilized by the oxyanion hole. From the intermediate to the product, the orientation of the His447 ring needs to be adjusted very slightly, and then, the proton transfers from His447 to the product, and the break of the scissile bond happens spontaneously. For the three-pronged oxyanion hole, it only makes two hydrogen bonds with the carbonyl oxygen at either the initial reactant or the final product state, but the third hydrogen bond is formed and stable at all transition and intermediate states during the catalytic process. At the intermediate state of the acylation reaction, a short and low-barrier hydrogen bond (LBHB) is found to be formed between two catalytic triad residues His447 and Glu334, and the spontaneous proton transfer between two residues has been observed. However, it is only about 1-2 kcal/mol stronger than the normal hydrogen bond. In comparison with previous theoretical investigations of the AChE catalytic mechanism, our current study clearly demonstrates the power and advantages of employing Born-Oppenheimer ab initio QM/MM MD simulations in characterizing enzyme reaction mechanisms.

Comparison of Two Metal-Dependent Pyruvate Aldolases Related by Convergent Evolution: Substrate Specificity, Kinetic Mechanism, and Substrate Channeling

HpaI and BphI are two pyruvate class II aldolases found in aromatic meta-cleavage degradation pathways that catalyze similar reactions but are not related in sequence. Steady-state kinetic analysis of the aldol addition reactions and product inhibition assays showed that HpaI exhibits a rapid equilibrium random order mechanism while BphI exhibits a compulsory order mechanism, with pyruvate binding first. Both aldolases are able to utilize aldehyde acceptors two to five carbons in length; however, HpaI showed broader specificity and had a preference for aldehydes containing longer linear alkyl chains or C2-OH substitutions. Both enzymes were able to bind 2-keto acids larger than pyruvate, but only HpaI was able to utilize both pyruvate and 2-ketobutanoate as carbonyl donors in the aldol addition reaction. HpaI lacks stereospecific control producing racemic mixtures of 4-hydroxy-2-oxopentanoate (HOPA) from pyruvate and acetaldehyde while BphI synthesizes only (4S)-HOPA. BphI is also able to utilize acetaldehyde produced by the reduction of acetyl-CoA catalyzed by the associated aldehyde dehydrogenase, BphJ. This aldehyde was directly channeled from the dehydrogenase to the aldolase active sites, with an efficiency of 84%. Furthermore, the BphJ reductive deacylation reaction increased 4-fold when BphI was catalyzing the aldol addition reaction. Therefore, the BphI-BphJ enzyme complex exhibits unique bidirectionality in substrate channeling and allosteric activation.

Ligand-bound Structures Provide Atomic Snapshots for the Catalytic Mechanism of d-Amino Acid Deacylase

d-tyrosyl-tRNATyr deacylase (DTD) is an editing enzyme that removes d-amino acids from mischarged tRNAs. We describe an in-depth analysis of the malaria parasite Plasmodium falciparum DTD here. Our data provide structural insights into DTD complexes with adenosine and d-amino acids. Bound adenosine is proximal to the DTD catalysis site, and it represents the authentic terminal adenosine of charged tRNA. DTD-bound d-amino acids cluster at three different subsites within the overall active site pocket. These subsites, called transition, active, and exit subsites allow docking, re-orientation, chiral selection, catalysis, and exit of the free d-amino acid from DTD. Our studies reveal variable modes of d-amino acid recognition by DTDs, suggesting an inherent plasticity that can accommodate all d- amino acids. An in-depth analysis of native, ADP-bound, and d- amino acid-complexed DTD structures provide the first atomic snapshots of ligand recognition and subsequent catalysis by this enzyme family. We have mapped sites for the deacylation reaction and mark possible routes for entry and egress of all substrates and products. We have also performed structure-based inhibitor discovery and tested lead compounds against the malaria parasite P. falciparum using growth inhibition assays. Our studies provide a comprehensive structural basis for the catalytic mechanism of DTD enzymes and have implications for inhibition of this enzyme in P. falciparum as a route to inhibiting the parasite.

Enantioselective biocatalytic reactions on (±)-aryl alkyl ketones with native and modified porcine pancreatic lipase

Porcine pancreatic lipase (PPL), pre-incubated with acetophenone in tetrahydrofuran, fails to recognize ortho- and para-acyloxy functions with respect to the nuclear carbonyl group in (±)-2,4-diacyloxyphenyl alkyl ketones and produces novel aryl alkyl ketones in moderate-to-highly optically active forms; this result supports the hypothesis on the mechanism of action of PPL in deacylation reactions on peracylated polyphenolics.

Deacylation reactions of 20-acetyl dinorcholanic lactones and 20,23-diacetyl furost-22-enes

We report the deacylation of (20 R)-20-acetyl-23,24-dinorcholanic lactones by hydrazine hydrate, under microwave irradiation in high yields. The elimination of the 20-acetyl group proceeded with retention of configuration which contrast with other proved deacylation methods that yield a mixture of diastereoisomers. In this way, unnatural (20 R)-23,24-dinorcholanic lactones can be produced rapidly on a large scale. Both (20 R)- and (20 S)-lactones were prepared starting from diosgenin, hecogenin and sarsasapogenin, in 72–80% overall yields.

Re‐examining the role of Lys67 in class C β‐lactamase catalysis

Lys67 is essential for the hydrolysis reaction mediated by class C beta-lactamases. Its exact catalytic role lies at the center of several different proposed reaction mechanisms, particularly for the deacylation step, and has been intensely debated. Whereas a conjugate base hypothesis postulates that a neutral Lys67 and Tyr150 act together to deprotonate the deacylating water, previous experiments on the K67R mutants of class C beta-lactamases suggested that the role of Lys67 in deacylation is mainly electrostatic, with only a 2- to 3-fold decrease in the rate of the mutant vs the wild type enzyme. Using the Class C beta-lactamase AmpC, we have reinvestigated the activity of this K67R mutant enzyme, using biochemical and structural studies. Both the rates of acylation and deacylation were affected in the AmpC K67R mutant, with a 61-fold decrease in k(cat), the deacylation rate. We have determined the structure of the K67R mutant by X-ray crystallography both in apo and transition state-analog complexed forms, and observed only minimal conformational changes in the catalytic residues relative to the wild type. These results suggest that the arginine side chain is unable to play the same catalytic role as Lys67 in either the acylation or deacylation reactions catalyzed by AmpC. Therefore, the activity of this mutant can not be used to discredit the conjugate base hypothesis as previously concluded, although the reaction catalyzed by the K67R mutant itself likely proceeds by an alternative mechanism. Indeed, a manifold of mechanisms may contribute to hydrolysis in class C beta-lactamases, depending on the enzyme (wt or mutant) and the substrate, explaining why different mutants and substrates seem to support different pathways. For the WT enzyme itself, the conjugate base mechanism may be well favored.

Calcium‐independent phospholipase A2‐mediated formation of 1,2‐diarachidonoyl‐glycerophosphoinositol in monocytes

Phagocytic cells exposed to exogenous arachidonic acid (AA) incorporate large quantities of this fatty acid into choline and ethanolamine glycerophospholipids, and into phosphatidylinositol (PtdIns). Utilizing liquid chromatography coupled to MS, we have characterized the incorporation of exogenous deuterated AA ([(2)H]AA) into specific PtdIns molecular species in human monocyte cells. A PtdIns species containing two exogenous [(2)H]AA molecules (1-[(2)H]AA-2-[(2)H]AA-glycero-3-phosphoinositol) was readily detected when human U937 monocyte-like cells and peripheral blood monocytes were exposed to [(2)H]AA concentrations as low as 160 nm to 1 mum. Bromoenol lactone, an inhibitor of Ca(2+)-independent phospholipase A(2) (iPLA(2)), diminished lyso-PtdIns levels, and almost completely inhibited the appearance of 1-[(2)H]AA-2-[(2)H]AA-glycero-3-phosphoinositol, suggesting the involvement of deacylation reactions in the synthesis of this phospholipid. De novo synthesis did not appear to be involved, as no other diarachidonoyl phospholipid or neutral lipid was detected under these conditions. Measurement of the metabolic fate of 1-[(2)H]AA-2-[(2)H]AA-glycero-3-phosphoinositol after pulse-labeling of the cells with [(2)H]AA showed a time-dependent, exponential decrease in the level of this phospholipid. These results identify 1-[(2)H]AA-2-[(2)H]AA-glycero-3-phosphoinositol as a novel, short-lived species for the initial incorporation of AA into the PtdIns class of cellular phospholipids in human monocytes.